The Next Era of Research Communication

From the days of actual research papers (before the digital age), to now where research papers are posted online first, not much has really changed in the way we communicate. We still use static images, formulas and a bunch of text to show what we have discovered in the laboratory.

This has definitely worked. However, I think (or I’d like to believe) we’re heading into a new era of how we share research. The rise of animations, GIFs and interactive visualizations is about to make reading scientific papers a little bit more fun.

So what has contributed to this movement? Of course, like any paradigm shift, several things accumulate to make it happen. But one of the major players is JavaScript and one library in particular: D3.js.

D3.js is a JavaScript library that makes it easy to manipulate HTML DOMs (Document Object Model). Using this library, the sky is the limit. You can build an insane amount of visualizations. The learning curve is a bit stiff, but the freedom it gives you is worth every minute spent learning how to use it properly.

LaTeX has been the ultimate publishing tool when it comes to scientific papers. LaTeX, pronounced lay-tek is an open source domain specific language. It was initially released in 1985 so it’s been around for a very, very long time. The norm is to usually author the papers in LaTeX and then convert them into PDFs where they will be consumed by the general readers.

So What’s Next?

There are several efforts going in the direction of interactive papers. Some consciously and some just evolving naturally by the sheer need of whoever is playing around with them.

MarkDown

MarkDown (MD) is a “text-to-html” conversion tool authored by John Gruber. MarkDown is widely used in the software development community (ex: README.md docs) and now slowly creeping into the statistics community with RMarkDown. Its syntax let’s you write in simple plain text and then converts it into a robust HTML page. Its very simple to learn and very convenient to use, thanks to it’s simplicity.

Finding a way to add animations/visualizations, not just GIFs to MarkDown might make sharing — at least drafts — a bit more pleasant and understandable.

PDBF

PDBF is probably the most interesting out of all of these. It’s three things at the same time. It’s a PDF document, an HTML page and an OVA file. What you get depends on where you open the file and what extension you give it. If you save it as a PDF, you get the static part of the document. If you save it as an HTML doc and open it in a browser, you get the dynamic and static part of the document. Meaning you can interact with the visualizations etc… And lastly, the OVA part of it let’s you add an entire virtual box to it so you can run an entire operating system out of it.

Online

Some new blogs, non-official publications and pre-print hubs are also starting to allow users and/contributors to add custom visualization by allowing them to write in HTML and add D3.js visualizations. The only thing with these is export and sharing beyond the Internet-connected browser. They are only viewable in the browser and good luck saving them into a single file. Crazy enough, I think they are the future. An Internet connection is as available as electricity (might be a stretch in some places) these days, so should you really download and save the research paper? Can’t you just read it in your browser, bookmark it and come back to it again if you need to, while enjoying the visualizations?

Edit: check out distill.pub, a publication that let’s you submit interactive articles on machine learning.